Cell Ranger3.0, printed on 12/10/2023
Goal: To find subgroups within broader cell types and larger clusters.
Loupe Cell Browser allows you to create your own cell subgroups, both via expression filtering and by manual selection. We will use both techniques here to try to identify substructure within the B cells in the AML tutorial dataset, and see if there are genes that distinguish those subgroups.
Let's return to the list of B cell markers (CD79A/CD79B). We know from before that those cells are in a general area within the t-SNE projection, but we want to create a subgroup of cells that are definitively CD79+. To do so, we will use the expression filter in the Gene/Feature Expression panel. By specifying a condition and numerical value, and pressing the Filter button, you will highlight the cells in your dataset that meet that criteria. The video below shows how we select all CD79a/b+ cells:
Clicking the Split View button reveals that the expression filter caught some cells from outside the main B cell cluster. For the purpose of this exercise, let's remove those cells from our B Cell "All Cells" group. Use the Lasso Selection tool from the toolbox, and select all the cells outside the main B cell cluster by dragging a shape around those cells, as shown below:
By zooming into the "All Cells" cluster, we can visually identify three, possibly four distinct subgroups. Let's reuse the lasso selection tool to create new subgroups, this time assigning cells a new cluster within the B Cells category:
We've now done some substantive exploration of this dataset. Let's finish the tutorial by learning how to save and share our work.